[gmx-users] Umbrella Sampling-gmx distance
rose rahmani
rose.rhmn93 at gmail.com
Thu Jan 11 09:43:27 CET 2018
Hi
i'm doing umbella sampling. whenever i use gmx distance after pulling in
V.5.1.4 , i wouldn't have proper dist.xvg file.for example; this my mdp
file for pulling:
integrator = md
dt = 0.001
nsteps = 2500000
nstxout = 5000
nstvout = 5000
nstfout = 500
nstlog = 500
nstenergy = 1000
nstxtcout = 1000
nstlist = 10
rlist = 1.5
cutoff_scheme = group
coulombtype = pme
rcoulomb = 1.5
vdwtype = Switch
rvdw_switch = 1.0
rvdw = 1.2
pcoupl = no
gen_vel = no
constraints = h-bonds
ns_type = grid
pbc = xy
freezegrps = WAL ZnS
freezedim = Y Y Y Y Y Y
energygrp-excl = WAL WAL ZnS ZnS
energygrps = SOL WAL ZnS Protein NA CL
nwall = 2
wall-atomtype = C C
wall-type = 9-3
wall-density = 150 150
wall-ewald-zfac = 3
ewald-geometry = 3dc
fourierspacing = 0.12
tcoupl = v-rescale
tc-grps = System
tau-t = 0.1
ref-t = 300
; Pull code
pull = yes
pull_ngroups = 2
pull_ncoords = 1
pull_group1_name = ZnS
pull_group2_name = Protein
pull_coord1_type = umbrella
pull_coord1_geometry = direction
pull_coord1_groups = 1 2
pull_coord1_dim = N N Y
pull_coord1_vec = 0 0 1
pull_coord1_rate = -0.001
pull_coord1_k = 5000
pull_coord1_start = yes
pull_nstxout = 10
and this is dist0.xvg
# This file was created Thu Jan 11 03:19:07 2018
# Created by:
# :-) GROMACS - gmx distance, VERSION 5.1.4 (-:
#
# Executable: /usr/local/gromacs/bin/gmx
# Data prefix: /usr/local/gromacs
# Command line:
# gmx distance -s pull.tpr -n index.ndx -f conf0.gro -oall dist0.xvg
# gmx distance is part of G R O M A C S:
#
#
¸<86><9e><8c>ð<88><9a><8d><8c>ò<9e><8b><8a><8d><9a>þ<8b>ü<8d><86><90><98><9a><91><96><9c>ì<8f><9a><9a><9b>
#
@ title "Distance"
@ xaxis label "Time (ps)"
@ yaxis label "Distance (nm)"
@TYPE xy
0.000 0.382 0.382 0.383 0.383 0.383 0.383 1.178
0.382 0.382 0.383 0.383 0.383 0.383 0.383 0.382
0.818 0.382 0.382 0.382 0.382 0.541 0.541 0.541
0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541
0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541
0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541
0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541
0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541
0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541
0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541
0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541
0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541
0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541
0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541
0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541
0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541
0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541
0.541 0.541 0.541 0.541 0.541 0.382 0.382 0.383
0.383 0.383 0.383 1.178 0.382 0.382 0.383 0.383
0.383 0.383 0.383 0.382 0.818 0.382 0.382 0.382
0.382 0.541 0.541 0.541 0.541 0.541 0.541 0.541
0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541
0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541
0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541
0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541
0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541
0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541
0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541
0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541
0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541
0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541
0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541
0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541
0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541
0.541 0.541 0.541 0.541 0.541 0.541 0.541 0.541
0.541 0.108 0.176 0.128 0.100 0.109 0.109 0.110
0.179 0.097 0.123 0.101 0.109 0.184
~
~
~
~
~
~
"dist0.xvg" [converted] 17L, 3161C
and summary distances.dat after using perl
0 0.382
1 0.382
2 .....
3 .....
.
.
.
----------------------------------------------------
i don't have this problem in V.4.5.4, this is mdp file for pulling:
integrator = md
dt = 0.002
nsteps = 1000000
nstxout = 5000
nstvout = 5000
nstfout = 500
nstlog = 500
nstenergy = 1000
nstxtcout = 1000
nstlist = 10
rlist = 1.5
coulombtype = pme
rcoulomb = 1.5
vdwtype = Switch
rvdw_switch = 1.0
rvdw = 1.2
pcoupl = no
gen_vel = no
constraints = h-bonds
ns_type = grid
pbc = xy
freezegrps = WAL ZnS
freezedim = Y Y Y Y Y Y
energygrp-excl = WAL WAL ZnS ZnS
energygrps = SOL WAL ZnS Protein NA CL
nwall = 2
wall-atomtype = C C
wall-type = 9-3
wall-density = 150 150
wall-ewald-zfac = 3
ewald-geometry = 3dc
fourierspacing = 0.12
tcoupl = v-rescale
tc-grps = System
tau-t = 0.1
ref-t = 300
; Pull code
pull = umbrella
pull_ngroups = 1
pull_group0 = ZnS
pull_group1 = Protein
pull_geometry = direction
pull_vec1 = 0 0 1
pull_dim = N N Y
pull_rate1 = -0.013
pull_k1 = 5000
pull_start = yes
pull_nstxout = 50
and this is dist0.xvg
# This file was created Thu Jan 11 03:36:46 2018
# by the following command:
# g_dist -s pull.tpr -n index.ndx -f conf0.gro -o dist0.xvg
#
# g_dist is part of G R O M A C S:
#
# Green Red Orange Magenta Azure Cyan Skyblue
#
@ title "Distance"
@ xaxis label "Time (ps)"
@ yaxis label "Distance (nm)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "|d|"
@ s1 legend "d\sx\N"
@ s2 legend "d\sy\N"
@ s3 legend "d\sz\N"
0.0000000 1.7630774 0.0185155 -0.0197599 -1.7628694
~
----------
i'm really confused,i don't what is the problem?!
would you please help me?
with regards
-Rose
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